.TH g_nmens 1 "Thu 26 Aug 2010" "" "GROMACS suite, VERSION 4.5"
.SH NAME
g_nmens - generates an ensemble of structures from the normal modes

.B VERSION 4.5
.SH SYNOPSIS
\f3g_nmens\fP
.BI "\-v" " eigenvec.trr "
.BI "\-e" " eigenval.xvg "
.BI "\-s" " topol.tpr "
.BI "\-n" " index.ndx "
.BI "\-o" " ensemble.xtc "
.BI "\-[no]h" ""
.BI "\-[no]version" ""
.BI "\-nice" " int "
.BI "\-xvg" " enum "
.BI "\-temp" " real "
.BI "\-seed" " int "
.BI "\-num" " int "
.BI "\-first" " int "
.BI "\-last" " int "
.SH DESCRIPTION
\&\fB g_nmens\fR generates an ensemble around an average structure
\&in a subspace which is defined by a set of normal modes (eigenvectors).
\&The eigenvectors are assumed to be mass\-weighted.
\&The position along each eigenvector is randomly taken from a Gaussian
\&distribution with variance kT/eigenvalue.


\&By default the starting eigenvector is set to 7, since the first six
\&normal modes are the translational and rotational degrees of freedom.
.SH FILES
.BI "\-v" " eigenvec.trr" 
.B Input
 Full precision trajectory: trr trj cpt 

.BI "\-e" " eigenval.xvg" 
.B Input
 xvgr/xmgr file 

.BI "\-s" " topol.tpr" 
.B Input
 Structure+mass(db): tpr tpb tpa gro g96 pdb 

.BI "\-n" " index.ndx" 
.B Input, Opt.
 Index file 

.BI "\-o" " ensemble.xtc" 
.B Output
 Trajectory: xtc trr trj gro g96 pdb 

.SH OTHER OPTIONS
.BI "\-[no]h"  "no    "
 Print help info and quit

.BI "\-[no]version"  "no    "
 Print version info and quit

.BI "\-nice"  " int" " 19" 
 Set the nicelevel

.BI "\-xvg"  " enum" " xmgrace" 
 xvg plot formatting: \fB xmgrace\fR, \fB xmgr\fR or \fB none\fR

.BI "\-temp"  " real" " 300   " 
 Temperature in Kelvin

.BI "\-seed"  " int" " \-1" 
 Random seed, \-1 generates a seed from time and pid

.BI "\-num"  " int" " 100" 
 Number of structures to generate

.BI "\-first"  " int" " 7" 
 First eigenvector to use (\-1 is select)

.BI "\-last"  " int" " \-1" 
 Last eigenvector to use (\-1 is till the last)

.SH SEE ALSO
.BR gromacs(7)

More information about \fBGROMACS\fR is available at <\fIhttp://www.gromacs.org/\fR>.
